M. Hallett, J. Lagergren, and A. Tofigh, Simultaneous identification of duplications and lateral transfers, Proceedings of the eighth annual international conference on Computational molecular biology , RECOMB '04, pp.347-356, 2004.
DOI : 10.1145/974614.974660

P. Górecki, Reconciliation problems for duplication, loss and horizontal gene transfer, Proceedings of the eighth annual international conference on Computational molecular biology , RECOMB '04, pp.316-325, 2004.
DOI : 10.1145/974614.974656

C. Conow, D. Fielder, Y. Ovadia, and R. Libeskind-hadas, Jane: a new tool for the cophylogeny reconstruction problem, Algorithms for Molecular Biology, vol.5, issue.1, p.16, 2010.
DOI : 10.1186/1748-7188-5-16

J. Doyon, C. Scornavacca, K. Y. Gorbunov, G. J. Szöll?-osi, V. Ranwez et al., An Efficient Algorithm for Gene/Species Trees Parsimonious Reconciliation with Losses, Duplications and Transfers, CG 2010, pp.93-108, 2010.
DOI : 10.1007/978-3-642-16181-0_9
URL : https://hal.archives-ouvertes.fr/lirmm-00818889

A. Tofigh, M. Hallett, and J. Lagergren, Simultaneous Identification of Duplications and Lateral Gene Transfers, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.8, issue.2, pp.517-535, 2011.
DOI : 10.1109/TCBB.2010.14

L. A. David and E. J. Alm, Rapid evolutionary innovation during an Archaean genetic expansion, Nature, vol.15, issue.7328, pp.93-96, 2011.
DOI : 10.1038/nature09649
URL : http://hdl.handle.net/1721.1/61263

M. S. Bansal, E. J. Alm, and M. Kellis, Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss, Bioinformatics, vol.28, issue.12, p.2012, 2012.
DOI : 10.1093/bioinformatics/bts225

M. Goodman, J. Czelusniak, G. W. Moore, R. A. Herrera, and G. Matsuda, Fitting the Gene Lineage into its Species Lineage, a Parsimony Strategy Illustrated by Cladograms Constructed from Globin Sequences, Systematic Zoology, vol.28, issue.2, pp.132-163, 1979.
DOI : 10.2307/2412519

R. D. Page, Extracting Species Trees From Complex Gene Trees: Reconciled Trees And Vertebrate Phylogeny, Molecular Phylogenetics and Evolution, vol.14, issue.1, pp.89-106, 2000.
DOI : 10.1006/mpev.1999.0676
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.18.1144

B. Ma, M. Li, and L. Zhang, From Gene Trees to Species Trees, SIAM Journal on Computing, vol.30, issue.3, pp.729-752, 2001.
DOI : 10.1137/S0097539798343362

L. Nakhleh, T. Warnow, and C. R. Linder, Reconstructing reticulate evolution in species, Proceedings of the eighth annual international conference on Computational molecular biology , RECOMB '04, pp.337-346, 2004.
DOI : 10.1145/974614.974659

L. Arvestad, J. Lagergren, and B. Sennblad, The gene evolution model and computing its associated probabilities, Journal of the ACM, vol.56, issue.2, 2009.
DOI : 10.1145/1502793.1502796

J. Doyon, V. Ranwez, V. Daubin, and V. Berry, Models, algorithms and programs for phylogeny reconciliation, Briefings in Bioinformatics, vol.12, issue.5, pp.392-400, 2011.
DOI : 10.1093/bib/bbr045
URL : https://hal.archives-ouvertes.fr/lirmm-00825041

Y. Ovadia, D. Fielder, C. Conow, and R. Libeskind-hadas, The Cophylogeny Reconstruction Problem Is NP-Complete, Journal of Computational Biology, vol.18, issue.1, pp.59-65, 2011.
DOI : 10.1089/cmb.2009.0240

R. Libeskind-hadas and M. A. Charleston, On the Computational Complexity of the Reticulate Cophylogeny Reconstruction Problem, Journal of Computational Biology, vol.16, issue.1, pp.105-117, 2009.
DOI : 10.1089/cmb.2008.0084

D. Durand, B. V. Halldorsson, and B. Vernot, A Hybrid Micro???Macroevolutionary Approach to Gene Tree Reconstruction, Journal of Computational Biology, vol.13, issue.2, pp.320-335, 2006.
DOI : 10.1089/cmb.2006.13.320

M. W. Hahn, Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution, Genome Biology, vol.8, issue.7, 2007.
DOI : 10.1186/gb-2007-8-7-r141

A. C. Berglund-sonnhammer, P. Steffansson, M. J. Betts, and D. A. Liberles, Optimal Gene Trees from Sequences and Species Trees Using a Soft Interpretation of Parsimony, Journal of Molecular Evolution, vol.3, issue.2, pp.240-250, 2006.
DOI : 10.1007/s00239-005-0096-1

W. Chang and O. Eulenstein, Reconciling Gene Trees with Apparent Polytomies, COCOON 2006, pp.235-244, 2006.
DOI : 10.1007/11809678_26

B. Vernot, M. Stolzer, A. Goldman, and D. Durand, Reconciliation with Non-Binary Species Trees, Journal of Computational Biology, vol.15, issue.8, pp.981-1006, 2008.
DOI : 10.1089/cmb.2008.0092
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3205801

R. Chaudhary, J. G. Burleigh, and O. Eulenstein, Algorithms for Rapid Error Correction for the Gene Duplication Problem, ISBRA 2011, pp.227-239, 2011.
DOI : 10.1089/cmb.1997.4.177

M. J. Sanderson, r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock, Bioinformatics, vol.19, issue.2, pp.301-302, 2003.
DOI : 10.1093/bioinformatics/19.2.301

A. Tofigh, Using Trees to Capture Reticulate Evolution, Lateral Gene Transfers and Cancer Progression, KTH Royal Institute of Technology, 2009.

J. Felsenstein, Inferring phylogenies, 2004.

D. E. Knuth, The Art of, Computer Programmingm, Sorting and Searching, vol.3, 1973.

D. G. Kendall, On the Generalized "Birth-and-Death" Process, The Annals of Mathematical Statistics, vol.19, issue.1, pp.1-15, 1948.
DOI : 10.1214/aoms/1177730285

A. Stamatakis, RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models, Bioinformatics, vol.22, issue.21, pp.2688-2690, 2006.
DOI : 10.1093/bioinformatics/btl446

D. F. Robinson and L. R. Foulds, Comparison of phylogenetic trees, Mathematical Biosciences, vol.53, issue.1-2, pp.131-147, 1981.
DOI : 10.1016/0025-5564(81)90043-2

S. Penel, A. M. Arigon, J. F. Dufayard, A. S. Sertier, V. Daubin et al., Databases of homologous gene families for comparative genomics, BMC Bioinformatics, vol.10, issue.Suppl 6, p.3, 2009.
DOI : 10.1186/1471-2105-10-S6-S3
URL : https://hal.archives-ouvertes.fr/lirmm-00400099